Re: [Pw_forum] Problems computing cholensky
Hi Laurens, The following input file is for a 24 atom anatase (001) slab separated by 12.5 angstroms of vacuum that relaxes without error messages (at least on my system). cat > $INFILE << EOF &CONTROL calculation = 'relax', restart_mode = 'from_scratch', prefix='$PREFIX', pseudo_dir='$PSEUDO_DIR', tstress=.true., tprnfor=.true., / &SYSTEM ibrav=0, nat=24, ntyp=2, ecutwfc=60, ecutrho=500, occupations='smearing', smearing='gaussian', degauss=0.01 / &ELECTRONS conv_thr = 1.0D-6, mixing_mode = 'local-TF', mixing_beta = 0.3d0, diagonalization = 'david', / &IONS ion_dynamics='bfgs', / &CELL cell_dynamics = 'bfgs', press=0.1d0, / ATOMIC_SPECIES Ti 47.88d0 Ti_PBE.UPF O 16.00d0 O_PBE.UPF CELL_PARAMETERS 14.36733988d0 0.0d0 0.0d0 0.0d0 7.18366994d0 0.0d0 0.0d0 0.0d0 41.94037d0 ATOMIC_POSITIONS angstrom Ti -0.00 -0.00 5.484694 Ti 1.900716 1.900716 10.331637 Ti -0.00 1.900716 7.908166 Ti 1.900716 -0.00 12.755109 O -0.00 -0.00 7.423471 O1.900716 1.900716 12.270415 O0.00 1.900716 9.846943 O1.900716 0.00 5.00 O1.900716 -0.00 10.816332 O0.00 1.900716 5.969388 O1.900716 1.900716 8.392860 O -0.00 -0.00 13.239803 Ti 3.801433 -0.00 5.484694 Ti 5.702149 1.900716 10.331637 Ti 3.801433 1.900716 7.908166 Ti 5.702149 -0.00 12.755109 O3.801433 -0.00 7.423471 O5.702149 1.900716 12.270415 O3.801433 1.900716 9.846943 O5.702149 0.00 5.00 O5.702149 -0.00 10.816332 O3.801433 1.900716 5.969388 O5.702149 1.900716 8.392860 O3.801433 -0.00 13.239803 K_POINTS automatic 4 4 1 0 0 0 EOF module load espresso/5.4.0 ibrun pw.x < $INFILE > $OUTFILE # Run the executable named pw.x rm *.igk *.wfc* rm -r *.save Will DeBenedetti Grad Student Cornell University On Sat, Feb 24, 2018 at 2:53 PM, Manu Hegde wrote: > Hi, > I do not know much about your system but looking quickly into the crystal > structure there is something that might be causing problem. Looks like you > have set ibrav=0, in that case you have to use card cell_parameters. A=xx > not required. Also double check ypur system with xcrysden before starting > the calculations. > Manu > (SFU) > > On Fri, Feb 23, 2018 at 10:19 AM, wrote: > >> Hello Laurens Siemons, >> >> Although I am not one of the experts, I had the same problem in one of >> the scf runs I was doing for a GW calculation. Because of the high >> number of bands and ecutwfc that I needed to use and in order to get >> any results, I had to run the simulation on 100 cores. The strange >> thing for me also was that the first one I tried run, but then nothing >> again. After a few weeks of trying I was notified by our cluster >> services that I should not use more than 60 cores as the I/O >> operations that are done by QE were too high and the disk could not >> cope. I gave up GW since then, but if there is a solution to this >> problem, I would like to hear it too :S >> >> >> Eleni >> >> >> Quoting Laurens Siemons : >> >> > Dear all, >> > >> > >> > I'm a master student chemistry and I'm using QE (v. 6.1) for a relax >> > calculation of a rutile 101 slab with a vacuum above it. >> > >> > I'm getting the famous error: >> > >> > >> > >> > >> %% >> > Error in routine cdiaghg (161): >> > problems computing cholesky >> > >> > >> %% >> > >> > I've read almost every related topic on the forum that I could find >> > and I tried a lot already to overcome this, like: >> > - changing values for ecutwfc and ecutrho >> > - changing mixing_beta >> > - changing functionals >> > - Tried to run the calcualtion with other input files (anatase 101, >> 001...) >> > - Changed diagonalization to 'cg' (In this case it calculates some >> > itterations but then crashes with the error: 'Error in routine >> > c_bands (1): >> too many bands are not converged') >> > >> > Nothing seems to help and I'm out of options... I even tried to run >> > a calculation of my predecessor (that has succeeded in the past) but >> > this also failed (he used an older version of QE though...). >> > >> > I'm postig my input file at the end here and I really hope somebody >> > can help me. >> > >> > Kind Regards, >> > Laurens Siemons >> > >> > &CONTROL >> > calculation = 'relax' >> > restart_mode = "from_scratch", >> > prefix = "testen", >> > pseudo_dir = >> > '/data/antwerpen/204/vsc20442/pseudo/pslibrary.1.0.0/wc/PSEU >> DOPOTENTIALS' >> > outdir = '
[Pw_forum] MoS2 valence bands
Hello all, I am trying to calculate the electronic band structure for monolayer MoS2 using quantum espresso.Mo and S both have 6 valence electrons, a total of 18 valence electrons in the unit cell. Hence I expect to have 9 valence bands but I see that I get 13 valence bands. I have not considered spin orbit interaction. Is it something I am assuming wrong ? Kindly let me know. thank you Gautam ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] LPZ functional in ld1.x
The logic (or lack of it) of XC names is a little bit tricky and needs to be revised a bit. On Fri, Feb 23, 2018 at 6:55 PM, wrote: > > I accidentally typed 'LPZ' instead of 'PZ' and the code run. > > > > Quoting Paolo Giannozzi : > > > I don't think there is any such functional (in fact the code is > > interpreting it as "no exchange" and "PZ=Perdew-Zunger correlation"). > Where > > did you find the output you report? > > > > Paolo > > > > On Fri, Feb 23, 2018 at 2:16 PM, wrote: > > > >> > >> Hello all, > >> > >> Does anyone know what the LPZ XC functional is? > >> > >> > >>scalar relativistic calculation > >> > >>atomic number is 42.00 > >>dft =LPZ lsd =0 sic =0 latt =0 beta=0.20 tr2=1.0E-14 > >>Exchange-correlation = LPZ ( 0 1 0 0 0 0) > >>mesh =1229 r(mesh) = 100.71859 a.u. xmin = -7.00 dx = 0.01250 > >>1 Ry = 13.60569193 eV, c = 137.03599966 > >> --- > >> > >> I can't find it in the functionals.f90 file or in libXC. > >> > >> Regards, > >> > >> > >> -- > >> Dr. Eleni Chatzikyriakou > >> Computational Physics lab > >> Aristotle University of Thessaloniki > >> elch...@auth.gr - tel:+30 2310 998109 > >> > >> ___ > >> Pw_forum mailing list > >> Pw_forum@pwscf.org > >> http://pwscf.org/mailman/listinfo/pw_forum > >> > > > > > > > > -- > > Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, > > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > > Phone +39-0432-558216, fax +39-0432-558222 > > > > -- > Dr. Eleni Chatzikyriakou > Computational Physics lab > Aristotle University of Thessaloniki > elch...@auth.gr - tel:+30 2310 998109 > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Error: Segmentation fault - invalid memory reference.
...and another one: does the original example work? On Sat, Feb 24, 2018 at 9:52 PM, Paolo Giannozzi wrote: > Line 227 of file export_upf.f90. There is just a piece of missing > information: code version > > On Sat, Feb 24, 2018 at 2:23 PM, BENYAHIA NEZHA > wrote: > >> Dear Quantum espresso developers and users, >> >> I'am trying to use the lda-1/2 for the first time to correct the band gap >> of Sb atom, i've followed the example of Si in the atomic code, using the >> inupt file: >> >> &input >>title='Sb', >>zed=51, >>config='[Kr] 5s2 5p3 4d10', >>iswitch=4 >>rel=2 >> / >> &test >> file_pseudo='Sb.pz.paw.UPF', >> file_pseudopw='Sb.lda.0.5.UPF', >> configts(1)='5s2 5p3 4d10', >> configts(2)='5s2 5p3 4d9.75', >> rcutv=1 >> / >> >> after that i exexuted this script ./job.test >> #!/bin/bash >> workd=./results/ >> mkdir -p $workd >> ./ld1.x Sb.lda.0.5.out >> mv *.out Sb.lda.0.5.UPF $workd >> rm -f *.wfc >> >> >> however i received this error: >> >> Program received signal SIGSEGV: Segmentation fault - invalid memory >> reference. >> Backtrace for this error: >> #0 0x7FD5A1A25777 >> #1 0x7FD5A1A25D7E >> #2 0x7FD5A115DCAF >> #3 0x42E9B0 in export_upf_ at export_upf.f90:227 (discriminator 3) >> #4 0x445453 in ld1_writeout_ at ld1_writeout.f90:92 >> #5 0x403632 in ld1 at ld1.f90:69 >> #6 0x7FD5A1148F44 >> ./test.job1: line 8: 9700 Segmentation fault (core dumped) $LD1 < >> Sb.lda.0.5.in > Sb.lda.0.5.out >> [6]+ Stopped mc >> >> >> Please help me to resolve this error, and i'll be so grateful. >> >> >> >> ___ >> Pw_forum mailing list >> Pw_forum@pwscf.org >> http://pwscf.org/mailman/listinfo/pw_forum >> > > > > -- > Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216 <+39%200432%20558216>, fax +39-0432-558222 > <+39%200432%20558222> > > -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Error: Segmentation fault - invalid memory reference.
Line 227 of file export_upf.f90. There is just a piece of missing information: code version On Sat, Feb 24, 2018 at 2:23 PM, BENYAHIA NEZHA wrote: > Dear Quantum espresso developers and users, > > I'am trying to use the lda-1/2 for the first time to correct the band gap > of Sb atom, i've followed the example of Si in the atomic code, using the > inupt file: > > &input >title='Sb', >zed=51, >config='[Kr] 5s2 5p3 4d10', >iswitch=4 >rel=2 > / > &test > file_pseudo='Sb.pz.paw.UPF', > file_pseudopw='Sb.lda.0.5.UPF', > configts(1)='5s2 5p3 4d10', > configts(2)='5s2 5p3 4d9.75', > rcutv=1 > / > > after that i exexuted this script ./job.test > #!/bin/bash > workd=./results/ > mkdir -p $workd > ./ld1.x Sb.lda.0.5.out > mv *.out Sb.lda.0.5.UPF $workd > rm -f *.wfc > > > however i received this error: > > Program received signal SIGSEGV: Segmentation fault - invalid memory > reference. > Backtrace for this error: > #0 0x7FD5A1A25777 > #1 0x7FD5A1A25D7E > #2 0x7FD5A115DCAF > #3 0x42E9B0 in export_upf_ at export_upf.f90:227 (discriminator 3) > #4 0x445453 in ld1_writeout_ at ld1_writeout.f90:92 > #5 0x403632 in ld1 at ld1.f90:69 > #6 0x7FD5A1148F44 > ./test.job1: line 8: 9700 Segmentation fault (core dumped) $LD1 < > Sb.lda.0.5.in > Sb.lda.0.5.out > [6]+ Stopped mc > > > Please help me to resolve this error, and i'll be so grateful. > > > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Problems computing cholensky
Hi,
I do not know much about your system but looking quickly into the crystal
structure there is something that might be causing problem. Looks like you
have set ibrav=0, in that case you have to use card cell_parameters. A=xx
not required. Also double check ypur system with xcrysden before starting
the calculations.
Manu
(SFU)
On Fri, Feb 23, 2018 at 10:19 AM, wrote:
> Hello Laurens Siemons,
>
> Although I am not one of the experts, I had the same problem in one of
> the scf runs I was doing for a GW calculation. Because of the high
> number of bands and ecutwfc that I needed to use and in order to get
> any results, I had to run the simulation on 100 cores. The strange
> thing for me also was that the first one I tried run, but then nothing
> again. After a few weeks of trying I was notified by our cluster
> services that I should not use more than 60 cores as the I/O
> operations that are done by QE were too high and the disk could not
> cope. I gave up GW since then, but if there is a solution to this
> problem, I would like to hear it too :S
>
>
> Eleni
>
>
> Quoting Laurens Siemons :
>
> > Dear all,
> >
> >
> > I'm a master student chemistry and I'm using QE (v. 6.1) for a relax
> > calculation of a rutile 101 slab with a vacuum above it.
> >
> > I'm getting the famous error:
> >
> >
> >
> >
> %%
> > Error in routine cdiaghg (161):
> > problems computing cholesky
> >
> >
> %%
> >
> > I've read almost every related topic on the forum that I could find
> > and I tried a lot already to overcome this, like:
> > - changing values for ecutwfc and ecutrho
> > - changing mixing_beta
> > - changing functionals
> > - Tried to run the calcualtion with other input files (anatase 101,
> 001...)
> > - Changed diagonalization to 'cg' (In this case it calculates some
> > itterations but then crashes with the error: 'Error in routine
> > c_bands (1): >> too many bands are not converged')
> >
> > Nothing seems to help and I'm out of options... I even tried to run
> > a calculation of my predecessor (that has succeeded in the past) but
> > this also failed (he used an older version of QE though...).
> >
> > I'm postig my input file at the end here and I really hope somebody
> > can help me.
> >
> > Kind Regards,
> > Laurens Siemons
> >
> > &CONTROL
> > calculation = 'relax'
> > restart_mode = "from_scratch",
> > prefix = "testen",
> > pseudo_dir =
> > '/data/antwerpen/204/vsc20442/pseudo/pslibrary.1.0.0/wc/
> PSEUDOPOTENTIALS'
> > outdir = '/data/antwerpen/204/vsc20442'
> > nstep = 100
> > /
> > &SYSTEM
> > ibrav = 0
> > A =4.59631
> > nat = 36
> > ntyp = 2
> > ecutwfc = 60
> > ecutrho = 600
> > /
> > &ELECTRONS
> > electron_maxstep = 300
> > mixing_beta = 0.10
> > conv_thr = 1.0d-8
> > mixing_mode = 'local-TF'
> > diago_thr_init = 1e-4
> > /
> > &IONS
> > ion_dynamics = 'bfgs'
> > ion_positions = 'default'
> > /
> > CELL_PARAMETERS {alat}
> > 1.000 0.000 0.640859733133753
> > 0.000 2.000 0.000
> > 0.000 0.000 3.845158398802518
> > ATOMIC_SPECIES
> >O 15.99900 O.wc-n-kjpaw_psl.1.0.0.UPF
> > Ti 47.86700 Ti.wc-spn-kjpaw_psl.1.0.0.UPF
> > ATOMIC_POSITIONS {crystal}
> > Ti -0.000 -0.000 0.075 0 0 0
> > Ti -0.000 -0.000 0.408
> > Ti -0.000 0.500 0.2416667
> > Ti -0.000 -0.000 0.2416667
> > Ti -0.000 0.500 0.075 0 0 0
> > Ti -0.000 0.500 0.408
> > Ti 0.500 0.250 0.075 0 0 0
> > Ti 0.500 0.250 0.408
> > Ti 0.500 0.750 0.2416667
> > Ti 0.500 0.250 0.2416667
> > Ti 0.500 0.750 0.075 0 0 0
> > Ti 0.500 0.750 0.408
> > O 0.3043030 0.1521515 0.0242828 0 0 0
> > O 0.3043030 0.1521515 0.35761616667
> > O 0.3043030 0.6521515 0.1909495
> > O 0.3043030 0.1521515 0.1909495
> > O 0.3043030 0.6521515 0.0242828 0 0 0
> > O 0.3043030 0.6521515 0.35761616667
> > O 0.6956970 0.3478485 0.4590505
> > O 0.6956970 0.3478485 0.2923838
> > O 0.6956970 0.8478485 0.12571716667 0 0 0
> > O 0.6956970 0.3478485 0.12571716667 0 0 0
> > O 0.6956970 0.847848
[Pw_forum] Error: Segmentation fault - invalid memory reference.
Dear Quantum espresso developers and users, I'am trying to use the lda-1/2 for the first time to correct the band gap of Sb atom, i've followed the example of Si in the atomic code, using the inupt file: &input title='Sb', zed=51, config='[Kr] 5s2 5p3 4d10', iswitch=4 rel=2 / &test file_pseudo='Sb.pz.paw.UPF', file_pseudopw='Sb.lda.0.5.UPF', configts(1)='5s2 5p3 4d10', configts(2)='5s2 5p3 4d9.75', rcutv=1 / after that i exexuted this script ./job.test #!/bin/bash workd=./results/ mkdir -p $workd ./ld1.x Sb.lda.0.5.out mv *.out Sb.lda.0.5.UPF $workd rm -f *.wfc however i received this error: Program received signal SIGSEGV: Segmentation fault - invalid memory reference. Backtrace for this error: #0 0x7FD5A1A25777 #1 0x7FD5A1A25D7E #2 0x7FD5A115DCAF #3 0x42E9B0 in export_upf_ at export_upf.f90:227 (discriminator 3) #4 0x445453 in ld1_writeout_ at ld1_writeout.f90:92 #5 0x403632 in ld1 at ld1.f90:69 #6 0x7FD5A1148F44 ./test.job1: line 8: 9700 Segmentation fault (core dumped) $LD1 < Sb.lda.0.5.in > Sb.lda.0.5.out [6]+ Stopped mc Please help me to resolve this error, and i'll be so grateful. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Problems computing cholensky
Dear Laurens, When I get this error, it is typically due to a parallelization issue. A quick fix that worked for me is using -ndiag 1 , so for example: pw.x_location -ndiag 1 output_file. Check the manual and forums for more details. Regards, Mostafa Youssef AUC, Egypt. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
